Continuous flow microfluidic devices have appeared to be a promising technology to automatise Polyelectrolytes multilayers (PEMs) coating on microbeads with repeatable and reliable results. However, no microfluidic devices have demonstrated PEMs coating on hydrogel beads yet. Here we introduce a new automated continuous flow microfluidic platform dedicated to the production of PEMs coated on monodispersed alginate beads. Microfluidic cartridges, based on a hybrid technology, are composed of two silicon chips bonded on a COC plate. Microfluidic channels are dry-etched with standard microelectronic technologies into silicon chips and grinded in plastic substrate. This microfluidic cartridge includes a micro-flow-focusing module to allow the generation of alginate inverse emulsion, a module to transfer the alginate droplets from oil to an aqueous calcium-based gelling solution and a multilaminar flow pillars chamber module to coat Poly-allylamine hydrochloride (PAH) solution. As a result, both optical and confocal microscopes images of monodisperse beads coated with one layer of covalently bonded fluorescent PAH are presented.